Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., isolated from maize root rhizosphere

Abstract

A facultative anaerobic, Gram-stain-positive, endospore-forming bacterium, isolated from the rhizosphere of maize roots (Zea mays), was taxonomically studied. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-79T clustered only loosely with Neobacillus species and showed the highest similarity to Neobacillus soli (97.9%). The 16S rRNA gene sequence similarities to the sequences of the type strains of other Neobacillus species were 97.5 % and below. Chemotaxonomic features supported the grouping of the strain to the Neobacillus group, e.g. the major fatty acids were C15 : 0 anteiso, C15 : 0 iso and C16 : 0, the polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid, the major quinone was menaquinone MK-7, and major compound in the polyamine pattern was spermidine. However, the JJ-79T genome assembly did not share most of the 11 conserved signature indels that are indicative of the genus Neobacillus . The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the JJ-79T genome assembly and those of the closest relative Bacillaceae type strains were <71, <71 and <25 %, respectively. Physiological and biochemical test results were also different from those of the most closely related Bacillaceae species. As a consequence, JJ-79T represents a novel genus for which we propose the name Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., with JJ-79T (=CIP 111885T=CCM 9045T) as the type strain.

AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species

“…With the exception of these species/strains, this CSI was not present in any other Bacillota or other bacteria in the top 500 hits. The observed results demonstrate the specificity of this CSI for Neobacillus and provide further evidence of the predictive ability of the CSIs to be present in other members of a specific taxon [67,68].…”

“…Due to their group (taxon)-specificity and predictive ability to be found in other members of the indicated group, the identified CSIs have provided important means for the demarcation of prokaryotic taxa of different ranks in molecular terms, thus aiding in the development of more robust classification schemes for prokaryotic organisms [38, 39, 47, 48, 50, 52, 53, 58]. The CSIs have now been identified for numerous prokaryotic taxa [38, 39, 47, 48, 50, 52, 53, 58, 63, 93, 94] and several investigators have used them for the classification of newly described species into specific taxa [54–56, 62, 67–74]. However, the lack of a convenient method for determining the presence or absence of known CSIs in genome sequences has limited the use of these molecular markers for taxonomic and diagnostic studies.…”

“…In the new classification scheme for Bacillus species, all newly described genera were reliably distinguished from each other (and other prokaryotic taxa) based on multiple identified CSIs which were specific for each of these genera [52,58]. Because of the predictive ability of the CSIs to be present in other members of these genera, the described CSIs have also been used by other investigators to assign newly described Bacillaceae species, as well as other species, into different genera [54][55][56][67][68][69][70][71][72][73][74]. Although the CSIs provide a very useful means for the circumscription of taxa of different ranks (specifically the genus-level clades), and for the assignment of new species into these genera based on the shared presence of CSIs, there is no convenient method available for determining the presence or absence of known taxon-specific CSIs in genome sequences.…”

Marinimicrococcus flavescens gen. nov., sp. nov., a new member of the family Geminicoccaceae, isolated from a marine sediment of the South China Sea

“…The ANI, DDH and AAI values are reported in Table S2. All of the estimated pairwise similarity values were far below the commonly accepted species delineation cut-offs [27] (ANI, 95%; AAI, 95%; DDH, 70 %) [28], suggesting that strain YIM 152171 T is a not-yet-described taxon.…”

Neobacillus terrae sp. nov., isolated from mountain soil

“…The genus Mesobacillus , a phylogenetically closely related genus with Neobacillus , was also proposed with Mesobacillus jeotgali as the type species via the reclassification of the Bacillus species clades [1]. In addition, recently, the genus Pseudoneobacillus , another closely related genus to Neobacillus , was proposed with Pseudoneobacillus rhizosphaerae as the type species [13]. Members of Neobacillus , Mesobacillus and Pseudoneobacillus are phylogenetically as well as chemotaxonomically similar, but it was reported that they can be differentiated by some conserved insertions or deletions (CSIs) of core protein sequences [1].…”